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Score: 14.00 |
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| Title: The spatial expression and regulation of transcription factors IDEF1 and IDEF2 .
| | Author: Kobayashi T Ogo Y Aung MS Nozoye T Itai RN Nakanishi H Yamakawa T Nishizawa NK | | Journal: Ann Bot Citation: V : 105 P : 1109-17 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20197292 Accession (PMID): 20197292 | | Abstract: BACKGROUND AND AIMS : Under conditions of low iron availability , rice plants induce genes involved in iron uptake and utilization .
The iron deficiency-responsive cis-acting element binding factors 1 and 2 ( IDEF1 and IDEF2 ) regulate transcriptional response to iron deficiency in rice roots .
Clarification of the functions of IDEF1 and IDEF2 could uncover the gene regulation mechanism .
METHODS : Spatial patterns of IDEF1 and IDEF2 expression were analysed by histochemical staining of IDEF1 and IDEF2 promoter-GUS transgenic rice lines .
Expression patterns of the target genes of IDEF1 and IDEF2 were analysed using transformants with induced or repressed expression of IDEF1 or IDEF2 grown in iron-rich or in iron-deficient solutions for 1 d .
KEY RESULTS : IDEF1 and IDEF2 were highly expressed in the basal parts of the lateral roots and vascular bundles .
IDEF1 and IDEF2 expression was dominant in leaf mesophyll and vascular cells , respectively .
These expression patterns were similar under both iron-deficient and iron-sufficient conditions .
IDEF1 was strongly expressed in pollen , ovaries , the aleurone layer and embryo .
IDEF2 was expressed in pollen , ovaries and the dorsal vascular region of the endosperm .
During seed germination , IDEF1 and IDEF2 were expressed in the endosperm and embryo .
Expression of IDEF1 target genes was regulated in iron-rich roots similar to early iron-deficiency stages .
In addition , the expression patterns of IDEF2 target genes were similar between iron-rich conditions and early or subsequent iron deficiency .
CONCLUSIONS : IDEF1 and IDEF2 are constitutively expressed during both vegetative and reproductive stages .
The spatial expression patterns of IDEF1 and IDEF2 overlap with their target genes in restricted cell types , but not in all cells .
The spatial expression patterns and gene regulation of IDEF1 and IDEF2 in roots are generally conserved under conditions of iron sufficiency and deficiency , suggesting complicated interactions with unknown factors for sensing and transmitting iron-deficiency signals .
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[ Sen. 4, subscore: 2.00 ]: METHODS : Spatial patterns of IDEF1 and IDEF2 expression were analysed by histochemical staining of IDEF1 and IDEF2 promoter-GUS transgenic rice lines .
[ Sen. 5, subscore: 2.00 ]: Expression patterns of the target genes of IDEF1 and IDEF2 were analysed using transformants with induced or repressed expression of IDEF1 or IDEF2 grown in iron-rich or in iron-deficient solutions for 1 d .
[ Sen. 2, subscore: 1.00 ]: The iron deficiency-responsive cis-acting element binding factors 1 and 2 ( IDEF1 and IDEF2 ) regulate transcriptional response to iron deficiency in rice roots .
[ Sen. 3, subscore: 1.00 ]: Clarification of the functions of IDEF1 and IDEF2 could uncover the gene regulation mechanism .
[ Sen. 6, subscore: 1.00 ]: KEY RESULTS : IDEF1 and IDEF2 were highly expressed in the basal parts of the lateral roots and vascular bundles .
[ Sen. 7, subscore: 1.00 ]: IDEF1 and IDEF2 expression was dominant in leaf mesophyll and vascular cells , respectively .
[ Sen. 9, subscore: 1.00 ]: IDEF1 was strongly expressed in pollen , ovaries , the aleurone layer and embryo .
[ Sen. 11, subscore: 1.00 ]: During seed germination , IDEF1 and IDEF2 were expressed in the endosperm and embryo .
[ Sen. 12, subscore: 1.00 ]: Expression of IDEF1 target genes was regulated in iron-rich roots similar to early iron-deficiency stages .
[ Sen. 14, subscore: 1.00 ]: CONCLUSIONS : IDEF1 and IDEF2 are constitutively expressed during both vegetative and reproductive stages .
[ Sen. 15, subscore: 1.00 ]: The spatial expression patterns of IDEF1 and IDEF2 overlap with their target genes in restricted cell types , but not in all cells .
[ Sen. 16, subscore: 1.00 ]: The spatial expression patterns and gene regulation of IDEF1 and IDEF2 in roots are generally conserved under conditions of iron sufficiency and deficiency , suggesting complicated interactions with unknown factors for sensing and transmitting iron-deficiency signals .
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Score: 11.00 |
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| Title: The rice transcription factor IDEF1 is essential for the early response to iron deficiency , and induces vegetative expression of late embryogenesis abundant genes .
| | Author: Kobayashi T Itai RN Ogo Y Kakei Y Nakanishi H Takahashi M Nishizawa NK | | Journal: Plant J Citation: V : 60 P : 948-61 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19737364 Accession (PMID): 19737364 | | Abstract: Higher plants maintain iron homeostasis by regulating the expression of iron ( Fe ) -related genes in accordance with Fe availability .
The transcription factor IDEF1 regulates the response to Fe deficiency in Oryza sativa ( rice ) by recognizing CATGC sequences within the Fe deficiency-responsive cis-acting element IDE1 .
To investigate the function of IDEF1 in detail , we analyzed the response to Fe deficiency in transgenic rice plants exhibiting induced or repressed IDEF1 expression .
Fe-deficiency treatment in hydroponic culture revealed that IDEF1 knock-down plants are susceptible to early-stage Fe deficiency , in contrast to IDEF1-induced plants .
Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2 , OsYSL15 , OsIRT1 , OsYSL2 , OsNAS1 , OsNAS2 , OsNAS3 and OsDMAS1 , just after the onset of Fe starvation .
However , this overall transactivation mediated by IDEF1 became less evident in subsequent stages .
Microarray and in-silico analyses revealed that genes positively regulated by IDEF1 , especially at the early stage , exhibit over-representation of CATGC and IDE1-like elements within the proximal promoter regions .
These results indicate the existence of early and subsequent responses to Fe deficiency , with the former requiring IDEF1 more specifically .
Proximal regions of IDEF1-regulated gene promoters also showed enrichment of RY elements ( CATGCA ) , which regulate gene expression during seed maturation .
The expression of several genes encoding late embryogenesis abundant proteins , including Osem , was induced in Fe-deficient roots and/or leaves in an IDEF1-dependent manner , suggesting a possible function of seed maturation-related genes in Fe-deficient vegetative organs .
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[ Sen. 3, subscore: 2.00 ]: To investigate the function of IDEF1 in detail , we analyzed the response to Fe deficiency in transgenic rice plants exhibiting induced or repressed IDEF1 expression .
[ Sen. 4, subscore: 2.00 ]: Fe-deficiency treatment in hydroponic culture revealed that IDEF1 knock-down plants are susceptible to early-stage Fe deficiency , in contrast to IDEF1-induced plants .
[ Sen. 2, subscore: 1.00 ]: The transcription factor IDEF1 regulates the response to Fe deficiency in Oryza sativa ( rice ) by recognizing CATGC sequences within the Fe deficiency-responsive cis-acting element IDE1 .
[ Sen. 5, subscore: 1.00 ]: Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2 , OsYSL15 , OsIRT1 , OsYSL2 , OsNAS1 , OsNAS2 , OsNAS3 and OsDMAS1 , just after the onset of Fe starvation .
[ Sen. 6, subscore: 1.00 ]: However , this overall transactivation mediated by IDEF1 became less evident in subsequent stages .
[ Sen. 7, subscore: 1.00 ]: Microarray and in-silico analyses revealed that genes positively regulated by IDEF1 , especially at the early stage , exhibit over-representation of CATGC and IDE1-like elements within the proximal promoter regions .
[ Sen. 8, subscore: 1.00 ]: These results indicate the existence of early and subsequent responses to Fe deficiency , with the former requiring IDEF1 more specifically .
[ Sen. 9, subscore: 1.00 ]: Proximal regions of IDEF1-regulated gene promoters also showed enrichment of RY elements ( CATGCA ) , which regulate gene expression during seed maturation .
[ Sen. 10, subscore: 1.00 ]: The expression of several genes encoding late embryogenesis abundant proteins , including Osem , was induced in Fe-deficient roots and/or leaves in an IDEF1-dependent manner , suggesting a possible function of seed maturation-related genes in Fe-deficient vegetative organs .
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Score: 9.00 |
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| Title: The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status .
| | Author: Kobayashi T Itai RN Aung MS Senoura T Nakanishi H Nishizawa NK | | Journal: Plant J Citation: V : 69 P : 81-91 Year: 2012 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub21880076 Accession (PMID): 21880076 | | Abstract: Iron is essential for most living organisms and its availability often determines survival and proliferation .
The Oryza sativa ( rice ) transcription factor IDEF1 plays a crucial role in regulating iron deficiency-induced genes involved in iron homeostasis .
In the present report , we found characteristic histidine-asparagine repeat and proline-rich regions in IDEF1 and its homolog in Hordeum vulgare ( barley ) , HvIDEF1 .
An immobilized metal ion affinity chromatography assay revealed that IDEF1 and HvIDEF1 bind to various divalent metals , including Fe ( 2+ ) and Ni ( 2+ ) . Recombinant IDEF1 protein expressed in Escherichia coli contained mainly Fe and Zn .
This metal-binding activity of IDEF1 was almost abolished by deletion of the histidine-asparagine and proline-rich regions , but DNA-binding and trans-activation functions were not impaired by the deletion .
Transgenic rice plants constitutively overexpressing IDEF1 without these metal-binding domains failed to cause pleiotropic effects conferred by overexpression of full-length IDEF1 , including a low germination rate , impaired seedling growth , tolerance to iron deficiency in hydroponic culture , and enhanced expression of various iron deficiency-inducible genes .
Impairment of the transcriptional regulation of IDEF1 by deletion of the metal-binding domains occurred primarily at an early stage of iron deficiency .
These results suggest that the histidine-asparagine and proline-rich regions in rice IDEF1 directly bind to divalent metals and sense the cellular metal ion balance caused by changes in iron availability .
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[ Sen. 4, subscore: 2.00 ]: An immobilized metal ion affinity chromatography assay revealed that IDEF1 and HvIDEF1 bind to various divalent metals , including Fe ( 2+ ) and Ni ( 2+ ) . Recombinant IDEF1 protein expressed in Escherichia coli contained mainly Fe and Zn .
[ Sen. 6, subscore: 2.00 ]: Transgenic rice plants constitutively overexpressing IDEF1 without these metal-binding domains failed to cause pleiotropic effects conferred by overexpression of full-length IDEF1 , including a low germination rate , impaired seedling growth , tolerance to iron deficiency in hydroponic culture , and enhanced expression of various iron deficiency-inducible genes .
[ Sen. 2, subscore: 1.00 ]: The Oryza sativa ( rice ) transcription factor IDEF1 plays a crucial role in regulating iron deficiency-induced genes involved in iron homeostasis .
[ Sen. 3, subscore: 1.00 ]: In the present report , we found characteristic histidine-asparagine repeat and proline-rich regions in IDEF1 and its homolog in Hordeum vulgare ( barley ) , HvIDEF1 .
[ Sen. 5, subscore: 1.00 ]: This metal-binding activity of IDEF1 was almost abolished by deletion of the histidine-asparagine and proline-rich regions , but DNA-binding and trans-activation functions were not impaired by the deletion .
[ Sen. 7, subscore: 1.00 ]: Impairment of the transcriptional regulation of IDEF1 by deletion of the metal-binding domains occurred primarily at an early stage of iron deficiency .
[ Sen. 8, subscore: 1.00 ]: These results suggest that the histidine-asparagine and proline-rich regions in rice IDEF1 directly bind to divalent metals and sense the cellular metal ion balance caused by changes in iron availability .
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Score: 7.00 |
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| Title: The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants .
| | Author: Kobayashi T Ogo Y Itai RN Nakanishi H Takahashi M Mori S Nishizawa NK | | Journal: Proc Natl Acad Sci U S A Citation: V : 104 P : 19150-5 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18025467 Accession (PMID): 18025467 | | Abstract: Iron is essential for most living organisms and is often the major limiting nutrient for normal growth .
Plants induce iron utilization systems under conditions of low iron availability , but the molecular mechanisms of gene regulation under iron deficiency remain largely unknown .
We identified the rice transcription factor IDEF1 , which specifically binds the iron deficiency-responsive cis-acting element IDE1 .
IDEF1 belongs to an uncharacterized branch of the plant-specific transcription factor family ABI3/VP1 and exhibits the sequence recognition property of efficiently binding to the CATGC sequence within IDE1 .
IDEF1 transcripts are constitutively present in rice roots and leaves .
Transgenic tobacco plants expressing IDEF1 under the control of the constitutive cauliflower mosaic virus 35S promoter transactivate IDE1-mediated expression only in iron-deficient roots .
Transgenic rice plants expressing an introduced IDEF1 exhibit substantial tolerance to iron deficiency in both hydroponic culture and calcareous soil .
IDEF1 overexpression leads to the enhanced expression of the iron deficiency-induced transcription factor gene OsIRO2 , suggesting the presence of a sequential gene regulatory network .
These findings reveal cis element/trans factor interactions that are functionally linked to the iron deficiency response .
Manipulation of IDEF1 also provides another approach for producing crops tolerant of iron deficiency to enhance food and biomass production in calcareous soils .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: We identified the rice transcription factor IDEF1 , which specifically binds the iron deficiency-responsive cis-acting element IDE1 .
[ Sen. 4, subscore: 1.00 ]: IDEF1 belongs to an uncharacterized branch of the plant-specific transcription factor family ABI3/VP1 and exhibits the sequence recognition property of efficiently binding to the CATGC sequence within IDE1 .
[ Sen. 5, subscore: 1.00 ]: IDEF1 transcripts are constitutively present in rice roots and leaves .
[ Sen. 6, subscore: 1.00 ]: Transgenic tobacco plants expressing IDEF1 under the control of the constitutive cauliflower mosaic virus 35S promoter transactivate IDE1-mediated expression only in iron-deficient roots .
[ Sen. 7, subscore: 1.00 ]: Transgenic rice plants expressing an introduced IDEF1 exhibit substantial tolerance to iron deficiency in both hydroponic culture and calcareous soil .
[ Sen. 8, subscore: 1.00 ]: IDEF1 overexpression leads to the enhanced expression of the iron deficiency-induced transcription factor gene OsIRO2 , suggesting the presence of a sequential gene regulatory network .
[ Sen. 10, subscore: 1.00 ]: Manipulation of IDEF1 also provides another approach for producing crops tolerant of iron deficiency to enhance food and biomass production in calcareous soils .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 7.00 |
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| Title: Dual regulation of iron deficiency response mediated by the transcription factor IDEF1 .
| | Author: Kobayashi T Nakanishi H Nishizawa NK | | Journal: Plant Signal Behav Citation: V : 5 P : Year: 2010 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub20023399 Accession (PMID): 20023399 | | Abstract: Higher plants respond to fluctuating Fe availability by regulating the expression of genes involved in Fe homeostasis .
Transcriptional responses to Fe deficiency in plants are mediated via various interactions between cisacting elements and trans-acting factors .
The transcription factor IDEF1 regulates the response to Fe deficiency in Oryza sativa ( rice ) by recognizing the CATGC sequence within the Fe deficiency-responsive cis-acting element IDE1 .
We recently presented evidence that IDEF1 mediates two-phase responses to Fe deficiency .
During the early stages of Fe deficiency , the majority of known Fe uptake/utilization-related genes are positively regulated by IDEF1 .
In subsequent stages , IDEF1-mediated regulation of these Fe uptake/utilization-related genes are less obvious .
In turn , expression of several Fe deficiency-induced genes encoding late embryogenesis abundant proteins is increasingly regulated by IDEF1 at the subsequent stages .
We propose a dual function of IDEF1 for Fe deficiency response , namely , ( i ) the coordinated transactivation of Fe utilizationrelated genes via CATGC-containing IDE1-like elements , especially at the early stage , and ( ii ) the transactivation of seed maturation-related genes via RY elements , especially during the subsequent stages of Fe deficiency .
IDEF1 appears to have evolved to mediate an interface between Fe deficiency-inducible and seed maturation-related gene expression .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: The transcription factor IDEF1 regulates the response to Fe deficiency in Oryza sativa ( rice ) by recognizing the CATGC sequence within the Fe deficiency-responsive cis-acting element IDE1 .
[ Sen. 4, subscore: 1.00 ]: We recently presented evidence that IDEF1 mediates two-phase responses to Fe deficiency .
[ Sen. 5, subscore: 1.00 ]: During the early stages of Fe deficiency , the majority of known Fe uptake/utilization-related genes are positively regulated by IDEF1 .
[ Sen. 6, subscore: 1.00 ]: In subsequent stages , IDEF1-mediated regulation of these Fe uptake/utilization-related genes are less obvious .
[ Sen. 7, subscore: 1.00 ]: In turn , expression of several Fe deficiency-induced genes encoding late embryogenesis abundant proteins is increasingly regulated by IDEF1 at the subsequent stages .
[ Sen. 8, subscore: 1.00 ]: We propose a dual function of IDEF1 for Fe deficiency response , namely , ( i ) the coordinated transactivation of Fe utilizationrelated genes via CATGC-containing IDE1-like elements , especially at the early stage , and ( ii ) the transactivation of seed maturation-related genes via RY elements , especially during the subsequent stages of Fe deficiency .
[ Sen. 9, subscore: 1.00 ]: IDEF1 appears to have evolved to mediate an interface between Fe deficiency-inducible and seed maturation-related gene expression .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
